September 23, 2012.
UC Santa Cruz bioinformatics team contributes to study from Cancer Genome Atlas project.
Joshua Stuart, UC Santa Cruz
One subtype of breast cancer shares many genetic features with high-grade serous ovarian cancer, a cancer that is very difficult to treat, according to researchers supported by the National Institutes of Health. The findings suggest that the two cancers are of similar molecular origin, which may facilitate the comparison of therapeutic data for subtypes of breast and ovarian cancers.
The study, using data generated as part of The Cancer Genome Atlas (TCGA), was published today (Sept. 23) in Nature. Researchers described new insights into the four standard molecular subtypes of breast cancer based on a comprehensive characterization of samples from 825 patients.
TCGA collaborators at the University of California, Santa Cruz, and the Buck Institute made significant contributions to the research, identifying molecular pathways that are affected by the genomic changes found in the patients? tumors. ?Pathway analysis is one of our strengths,? said Joshua Stuart, associate professor of biomolecular engineering in UCSC?s Baskin School of Engineering. ?The analysis points to common molecular circuitry between cancers arising in different tissues. Such connections may inform us about new directions for therapy.?
A key tool for pathway analysis is a software program called PARADIGM, developed at UCSC by a team led by Stuart and David Haussler, distinguished professor of biomolecular engineering and director of the Center for Biomolecular Science and Engineering. PARADIGM enables researchers to assess the consequences of a mutation and identify different genetic changes that affect a common molecular pathway. ?We?ve been able to read mutations but we haven?t been able to understand them,? Haussler said. ?PARADIGM allows us to look at multiple sources of data from patient samples and figure out which genetic pathways are altered from their normal function.?
TCGA, which involves more than 150 researchers working at dozens of institutions across the country, is in the midst of a five-year effort aimed at generating comprehensive, multidimensional maps of the key genomic changes in major types and subtypes of at least 20 different cancer types. The research ? which has already reported on glioblastoma multiforme (a type of brain cancer), serous ovarian cancer, colorectal cancer and lung squamous cell cancer ? is expected to result in a flood of discoveries that could lead to more powerful and personalized treatments based on targeting the genetic vulnerabilities of tumors.
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